We used techniques of immunogenetics and molecular biology to study the genes for rabbit immunoglobulins, and other genes including the RAG-1 and RAG-2 which are necessary for gene rearrangements to occur during lymphocyte development. We investigated the development of anatomical sites such as appendix follicles and germinal centers in gut associated lymphoid tissues and the regulated expression and sequence diversification of Ig genes during lymphoid cell development. Lectins allowed us to dissect rabbit appendix follicles and germinal centers into subcompartments based on local expression of glycosylated cell surface receptors. We proposed that in early development, the functional role of the rabbit appendix may be similar to that of the chicken bursa or sheep ileal Peyer's patch. The rabbit appendix, however, does not involute but may change from a site of primary variable region diversification to a site of secondary lymphoid responses. IgM associated B cell receptor molecules were found on rabbit B cells as heteromeric structures with nonreduced molecular weights of approximately 75 kDa and 135 kDa composed of 37 and 42 kDa subunits. Immunological studies with monoclonal antibodies suggested that these proteins are the rabbit homologues of murine Ig-beta (B29) and Ig-alpha (mb-1). Whereas B cells with rearranged VH1 predominate in normal rabbits, in homozygous Alicia mutant rabbits (ali/ali) the VH1 gene is deleted and B cells with upstream VH genes rearrange. We found differences between appendix cells from normal and ali/ali rabbits based on immunohistochemistry patterns and cell trafficking analyses. The trafficking patterns of appendix cells found in 6 week normals were similar to those found in 11 week old ali/ali. A higher proportion of B cells expressing the a2 allotype may receive strong signals to survive rather than undergo apoptosis. The a2 allotype probably plays functions role(s) in selection and effective expansion of B cells in the appendix.